Spray slow cooker insert with non-stick cooking spray. Add chicken to slow cooker insert and pour2 cups of enchilada sauce over the chicken. Cook on High setting for 4 hours or low setting for 8 hours. Shred chicken with a fork in the enchilada sauce. Drain green chilis and add to the chicken along with the diced onion. Mix well to combine.
Preheat oven to 350º F.
Spray a 9x13 baking dish with non-stick cooking spray.
Spoon chicken mixture into the center of each flour tortilla. Top with about ½ cup grated cheese and fold two ends of tortilla over the filled center. Place the tortilla seam side down into the baking dish. Repeat until all tortillas have been filled.
Pour remaining enchilada sauce over the assembled tortillas. Top with grated cheese. Place in oven and bake for about 20 minutes, until cheese has melted thoroughly and has become bubbly.
Garnish with green onions or cilantro, if desired.